S12DT256 can only run at 25MHz bus either when a "Pierce" oscillator circuit or when an external oscillator is used. If you are using a "Colpitts" oscillator, it will not work. This is described in detail in the manual.
What you likely are measuring on ECLK is "self clock mode", also known as "limp-home". When the S12 finds out that the oscillator is malfunctioning, it is using an internal inaccurate oscillator instead. This internal oscillator is typically around 2-4MHz, something like that. You could try to disable self clock mode and see if the bus clock dies entirely.
If you are in self clock mode, it means that your oscillator is malfunctioning. Apart from the need of a "Pierce" oscillator, you need to check are the PORTE:7 pin, which selects between Colpitts/Pierce. You will need an external pull-down on this pin.
I suppose it could also be related to the PLL, but that is less likely.
(Soldering of the crystal is the most common problem)